Someone knew that that roof had been leaking around that chimmney.
There was suppost to be step flashing, then counter flashing, not globs of roofing tar.
It would be best to repair this as the new roof is being installed or there's a very real chance of the new flashing being damaged as the new roof goes on if you do it later.
I just hate it when someone adds a second layer of shingles. It's now going to cost you twice as much to have the shingles removed and desposed of.
If you plan on staying in this house do not go with those cheap 3 tab shingles again, use architucural instead.
There going to last far longer, look better and less change of blowing off or leaking.